Map impacts for all impacted species

library(raster)
source('https://raw.githubusercontent.com/oharac/src/master/R/common.R')

source(here('common_fxns.R'))

library(animation)

reload <- FALSE

1 Summary

Create a species richness map for only the species included in this assessment.

Combine taxa-level impact and refugia maps to create maps of number of species impacted per cell, per year, and species in refugia (i.e., zero impact) per cell, per year.

Plot maps as animated rasters, both by absolute numbers of species impacted in a location and by proportion of species.

2 Methods

2.1 Create species richness map for this assessment

Set up the dataframe of species to include. By taxon, load all species range maps, smash down to taxon-level species richness; then combine these for a total species richness.

2.2 Setup for mapping across all taxa

For each combination of climate/no climate and impacts/refugia:

• gather all taxa-level map files into a raster stack
• collapse the stack using calc(fun = sum, na.rm = TRUE)
• animate over the years

2.3 Create impact map for all included spp, non-climate

2.4 Create impact map for all included spp, climate only

2.5 Create refugia map for all included spp, non-climate

2.6 Create refugia map for all included spp, climate only